Structure and dynamics of the crenarchaeal nucleoid

2013 ◽  
Vol 41 (1) ◽  
pp. 321-325 ◽  
Author(s):  
Rosalie P.C. Driessen ◽  
Remus Th. Dame
Keyword(s):  
Gene Regulation ◽  
Chromatin Structure ◽  
Molecular Properties ◽  
Present Review ◽  
Structure And Dynamics ◽  
Architectural Proteins ◽  
Chromatin Proteins

Crenarchaeal genomes are organized into a compact nucleoid by a set of small chromatin proteins. Although there is little knowledge of chromatin structure in Archaea, similarities between crenarchaeal and bacterial chromatin proteins suggest that organization and regulation could be achieved by similar mechanisms. In the present review, we describe the molecular properties of crenarchaeal chromatin proteins and discuss the possible role of these architectural proteins in organizing the crenarchaeal chromatin and in gene regulation.

The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme

2008 ◽  
Vol 389 (4) ◽  
pp. 323-331 ◽  
Author(s):  
David Umlauf ◽  
Peter Fraser ◽  
Takashi Nagano
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chromatin Structure ◽  
Genome Architecture ◽  
Paradoxical Situation ◽  
Intergenic Regions ◽  
Non Coding Rnas ◽  
Variations On A Theme

Abstract Transcriptome studies have uncovered a plethora of non-coding RNAs (ncRNA) in mammals. Most originate within intergenic regions of the genome and recent evidence indicates that some are involved in many different pathways that ultimately act on genome architecture and gene expression. In this review, we discuss the role of well-characterized long ncRNAs in gene regulation pointing to their similarities, but also their differences. We will attempt to highlight a paradoxical situation in which transcription is needed to repress entire chromosomal domains possibly through the action of ncRNAs that create nuclear environments refractory to transcription.

scholarly journals The bacterial chromatin protein HupA can remodel DNA and associates with the nucleoid in Clostridium difficile

2018 ◽  
Author(s):  
Ana M. Oliveira Paiva ◽  
Annemieke H. Friggen ◽  
Liang Qin ◽  
Roxanne Douwes ◽  
Remus T. Dame ◽  
...  
Keyword(s):  
Protein A ◽  
Chromatin Protein ◽  
Chromosomal Organization ◽  
Cellular Processes ◽  
Hu Proteins ◽  
Architectural Proteins ◽  
Chromatin Proteins

AbstractThe maintenance and organization of the chromosome plays an important role in the development and survival of bacteria. Bacterial chromatin proteins are architectural proteins that bind DNA, modulate its conformation and by doing so affect a variety of cellular processes. No bacterial chromatin proteins of C. difficile have been characterized to date.Here, we investigate aspects of the C. difficile HupA protein, a homologue of the histone-like HU proteins of Escherichia coli. HupA is a 10 kDa protein that is present as a homodimer in vitro and self-interacts in vivo. HupA co-localizes with the nucleoid of C. difficile. It binds to the DNA without a preference for the DNA G+C content. Upon DNA binding, HupA induces a conformational change in the substrate DNA in vitro and leads to compaction of the chromosome in vivo.The present study is the first to characterize a bacterial chromatin protein in C. difficile and opens the way to study the role of chromosomal organization in DNA metabolism and on other cellular processes in this organism.

ATRX in chromatin assembly and genome architecture during development and disease

2011 ◽  
Vol 89 (5) ◽  
pp. 435-444 ◽  
Author(s):  
Nathalie G. Bérubé
Keyword(s):  
Gene Regulation ◽  
Chromatin Remodeling ◽  
Chromatin Structure ◽  
Higher Order ◽  
Chromatin Assembly ◽  
Genome Architecture ◽  
Chromatin Conformation ◽  
Mammalian Development ◽  
Mitosis And Meiosis

The regulation of genome architecture is essential for a variety of fundamental cellular phenomena that underlie the complex orchestration of mammalian development. The ATP-dependent chromatin remodeling protein ATRX is emerging as a key regulatory component of nucleosomal dynamics and higher order chromatin conformation. Here we provide an overview of the role of ATRX at chromatin and during development, and discuss recent studies exposing a repertoire of ATRX functions at heterochromatin, in gene regulation, and during mitosis and meiosis. Exciting new progress on several fronts suggest that ATRX operates in histone variant deposition and in the modulation of higher order chromatin structure. Not surprisingly, dysfunction or absence of ATRX protein has devastating consequences on embryonic development and leads to human disease.

scholarly journals The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 92 ◽  
Author(s):  
Narasimharao Nalabothula ◽  
Graham McVicker ◽  
John Maiorano ◽  
Rebecca Martin ◽  
Jonathan K Pritchard ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Chromatin Structure ◽  
Architectural Proteins

scholarly journals The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite

2017 ◽  
Vol 33 (5) ◽  
pp. 364-377 ◽  
Author(s):  
Gayani Batugedara ◽  
Xueqing M. Lu ◽  
Evelien M. Bunnik ◽  
Karine G. Le Roch
Keyword(s):  
Gene Regulation ◽  
Chromatin Structure ◽  
Malaria Parasite ◽  
Human Malaria Parasite ◽  
Human Malaria

scholarly journals CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Martin Franke ◽  
Elisa De la Calle-Mustienes ◽  
Ana Neto ◽  
María Almuedo-Castillo ◽  
Ibai Irastorza-Azcarate ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chromatin Structure ◽  
Zebrafish Model ◽  
Developmental Gene Expression ◽  
Chromatin Interactions ◽  
Fundamental Requirement ◽  
Regulatory Landscapes

AbstractCoordinated chromatin interactions between enhancers and promoters are critical for gene regulation. The architectural protein CTCF mediates chromatin looping and is enriched at the boundaries of topologically associating domains (TADs), which are sub-megabase chromatin structures. In vitro CTCF depletion leads to a loss of TADs but has only limited effects over gene expression, challenging the concept that CTCF-mediated chromatin structures are a fundamental requirement for gene regulation. However, how CTCF and a perturbed chromatin structure impacts gene expression during development remains poorly understood. Here we link the loss of CTCF and gene regulation during patterning and organogenesis in a ctcf knockout zebrafish model. CTCF absence leads to loss of chromatin structure and affects the expression of thousands of genes, including many developmental regulators. Our results demonstrate the essential role of CTCF in providing the structural context for enhancer-promoter interactions, thus regulating developmental genes.

scholarly journals Chromatin and oxygen sensing in the context of JmjC histone demethylases

2014 ◽  
Vol 462 (3) ◽  
pp. 385-395 ◽  
Author(s):  
Alena Shmakova ◽  
Michael Batie ◽  
Jimena Druker ◽  
Sonia Rocha
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Human Disease ◽  
Current Knowledge ◽  
Oxygen Sensors ◽  
Present Review ◽  
Histone Demethylases ◽  
Missing Link ◽  
Stressful Condition

Responding appropriately to changes in oxygen availability is essential for multicellular organism survival. Molecularly, cells have evolved intricate gene expression programmes to handle this stressful condition. Although it is appreciated that gene expression is co-ordinated by changes in transcription and translation in hypoxia, much less is known about how chromatin changes allow for transcription to take place. The missing link between co-ordinating chromatin structure and the hypoxia-induced transcriptional programme could be in the form of a class of dioxygenases called JmjC (Jumonji C) enzymes, the majority of which are histone demethylases. In the present review, we will focus on the function of JmjC histone demethylases, and how these could act as oxygen sensors for chromatin in hypoxia. The current knowledge concerning the role of JmjC histone demethylases in the process of organism development and human disease will also be reviewed.

Nucleosome dynamics

2006 ◽  
Vol 73 ◽  
pp. 109-119 ◽  
Author(s):  
Chris Stockdale ◽  
Michael Bruno ◽  
Helder Ferreira ◽  
Elisa Garcia-Wilson ◽  
Nicola Wiechens ◽  
...  
Keyword(s):  
High Resolution ◽  
Chromatin Structure ◽  
Current Knowledge ◽  
Dynamic Properties ◽  
Structure And Dynamics ◽  
Nucleosome Dynamics ◽  
Sharp Focus ◽  
Recent Advances ◽  
Insight Into ◽  
Chromatin Structure And Dynamics

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.

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